Methodology:
Sampled 271 birds from 16 populations. Samples include both fresh and 142 museum samples. Fresh samples were obtained mainly by mist-netting, but also occasionally by 143 sampling a single chick from every nest.
DNA was extracted with the standard phenol-chloroform method. Museum samples were extracted in a separate room using a fume hood with UV-light exposure prior to 147 the extraction.
Seven microsatellite loci; Lox1, Lox2 and Lox8 (Piertney et al. 1998), Ppi2 (Martínez et 148 al. 1999), Pocc6 (Bensch et al. 1997), Pdo5 (Griffith et al. 1999) and Pk12 (GenBank accession no. 149 AF041466) were amplified using the procedure detailed in Barrientos et al. (2009b). Microsatellites 150 were run on ABI3730 and scored with GeneMapper v. 3.7 (Applied Biosystems, Foster City, CA, USA). 151 Part of the mitochondrial control region was amplified using primers TrfinchL20 and 152 passeriformesH830 which amplify most of 153 domains I and II of the control region. The museum samples were amplified in two or three fragments using primers TrfinchL20 and TrfinchH465, TrfinchL410 and PasseriformesH830, TrfinchL20 and 155 TrfinchH262, TrfinchL208 and TrfinchH465, TrfinchL410 and TrfinchH649 or TrfinchL585 and 156 PasseriformesH830.
PCR was performed in 10 μl volumes 157 containing about 50 ng of template DNA (1-5μl) , 0.5 μM of each primer (0.5 μl each), 0.2 mM of each 158 dNTP (1 μl), 1 μL of 10 x PCR buffer (2.0 mM MgCl2) and 0.06 μl of DNA-polymerase (Biotools, 5U/ 159 μl). The PCR protocol was 94ºC for 2 min followed by 37 cycles of 94ºC for 30 s, 50ºC for 45 s and 160 72ºC for 30 s with a final extension in 72ºC for 5 min. The Egyptian samples required a secondary PCR 161 using 1 μL of the primary PCR product as template. Sequencing of the PCR-products was performed 162 with BigDye v. 3.1 using primers TrfinchH262, TrfinchH465, TrfinchL410, TrfinchL585 or 163 PasseriformesH830. Half of the museum samples were sequenced twice to check for consistency of the 164 sequences. Sequencing reactions were run on an ABI3730. All sequences are available in GenBank 165 (accession numbers JX452830-JX453004 and JX453005-JX453016).